In this study, the associations between ISSR markers with some agronomic traits in 22 ispaghula ecotypes were used by stepwise regression analysis. The results of stepwise regression analysis showed a significant association between traits and some of loci markers positions. For some traits was detected more than one informative marker. Totally 90 informative ISSR markers were revealed that due to the associated of some markers in control of several traits, finally, the 48 markers were significantly associated with traits. The UBC816-2, UBC826-2 and UBC826-3 markers showed a significant correlation with grain yield and controlled 53.5% of the phenotypic variation. Among the ISSR primers, special attention should be drawn to primer UBC811 and UBC813-11 marker, because of the highest associated had exist between this primer and this marker with the studied traits. Some of these markers were associated with more than one trait that these traits had very close linkage together or possibly were controlled by pleiotropic effects. These primers have been found useful for improved Ispaghula.